First-choice custodian Sam Slocombe went off with an arm injury after just eight minutes and 30 minutes later his replacement, Jamie Severn, was stretchered off in agony and taken to hospital with a suspected fractured arm.
That forced centre-back Andy Boyce to take over the gloves as a makeshift keeper after new-look Scunthorpe had impressed in the early stages with home debuts for full-back Jordan Clarke, winger Jacob Murphy and striker Tom Hopper.
It was against the run of play when City opened the scoring in the 36th minute when Jay Emmanuel-Thomas netted from the penalty spot after Boyce had impeded giant striker Matt Smith.
Scunthorpe had gone close to a first minute lead when a goalbound shot from Neal Bishop was scrambled away by centre-back Luke Ayling.
With Boyce growing in confidence with the gloves, Scunthorpe surged forward for much of the second half searching for an equaliser.
But their luck was out again and it was City who made the game safe with a second goal in the 85th minute from Luke Freeman.